JUQUEEN: IBM Blue Gene/Q® Supercomputer System at the Jülich Supercomputing Centre

JUQUEEN is a high-scaling supercomputer funded mainly by the Gauss Centre for Supercomputing and by Helmholtz Association and is hosted by the Jülich Supercomputing Centre. It is a 28 rack, IBM Blue Gene/Q® system combining 28,672 compute nodes through a high-speed network providing an overall peak performance of 5.9 Petaflops

Performance Optimization Strategies for Transactional Memory Applications

This thesis presents tools for Transactional Memory (TM) applications that cover multiple TM systems (Software, Hardware, and hybrid TM) and use information of all different layers of the TM software stack. Therefore, this thesis addresses a number of challenges to extract static information, information about the run time behavior, and expert-level knowledge to develop these new methods and strategies for the optimization of TM applications

Boosting performance of transactional memory through transactional read tracking and set associative locks

Multi-core processors have become so prevalent in server, desktop, and even embedded systems that they are considered the norm for modem computing systems. The trend is likely toward many-core processors with many more than just 2, 4, or 8 cores per CPU. To benefit from the increasing number of cores per chip, application developers have to develop parallel programs [1]. Traditional lock-based programming is too difficult and error prone for most of programmers and is the domain of experts. Deadlock, race, and other synchronization bugs are some of the challenges of lock-based programming. To make parallel programming mainstream, it is necessary to adapt parallel programming by the majority of programmers and not just experts, and thus simplifying parallel programming has become an important challenge. Transactional Memory (TM) is a promising programming model for managing concurrent accesses to the shared memory locations. Transactional memory allows a programmer to specify a section of a code to be "'transactional", and the underlying system guarantees atomic execution of the code. This simplifies parallel programming and reduces the possibility of synchronization bugs. This thesis develops several software- and hardware-based techniques to improve performance of existing transactional memory systems. The first technique is Transactional Read Tracking (TRT). TRT is a software-based approach that employs a locking mechanism for transactional read and write operations. The performance of TRT depends on memory access patterns of applications. In some cases, TRT falls behind the baseline scheme. To further improve performance of TRT, we introduce two hybrid methods that dynamically switches between TRT and the baseline scheme based on applications’ behavior. The second optimization technique is Set Associative Lock (SAL). Memory locations are mapped to a lock table in order to synchronize accesses to the shared memory locations. Direct mapped lock tables usually result in collision which leads to false aborts. In SAL, we increase associativity of the lock table to reduce false abort. While SAL improves performance in most of the applications, in some cases, it increases execution time due to overhead of lock tables in software. To cope with this problem, we propose Hardware-SAL (HW-SAL) which moves the set associative lock table to the hardware. As such, true power of set associativity will be harnessed without sacrificing performance

Towards lightweight and high-performance hardware transactional memory

Conventional lock-based synchronization serializes accesses to critical sections guarded by the same lock. Using multiple locks brings the possibility of a deadlock or a livelock in the program, making parallel programming a difficult task. Transactional Memory (TM) is a promising paradigm for parallel programming, offering an alternative to lock-based synchronization. TM eliminates the risk of deadlocks and livelocks, while it provides the desirable semantics of Atomicity, Consistency, and Isolation of critical sections. TM speculatively executes a series of memory accesses as a single, atomic, transaction. The speculative changes of a transaction are kept private until the transaction commits. If a transaction can break the atomicity or cause a deadlock or livelock, the TM system aborts the transaction and rolls back the speculative changes. To be effective, a TM implementation should provide high performance and scalability. While implementations of TM in pure software (STM) do not provide desirable performance, Hardware TM (HTM) implementations introduce much smaller overhead and have relatively good scalability, due to their better control of hardware resources. However, many HTM systems support only the transactions that fit limited hardware resources (for example, private caches), and fall back to software mechanisms if hardware limits are reached. These HTM systems, called best-effort HTMs, are not desirable since they force a programmer to think in terms of hardware limits, to use both HTM and STM, and to manage concurrent transactions in HTM and STM. In contrast with best-effort HTMs, unbounded HTM systems support overflowed transactions, that do not fit into private caches. Unbounded HTM systems often require complex protocols or expensive hardware mechanisms for conflict detection between overflowed transactions. In addition, an execution with overflowed transactions is often much slower than an execution that has only regular transactions. This is typically due to restrictive or approximative conflict management mechanism used for overflowed transactions. In this thesis, we study hardware implementations of transactional memory, and make three main contributions. First, we improve the general performance of HTM systems by proposing a scalable protocol for conflict management. The protocol has precise conflict detection, in contrast with often-employed inexact Bloom-filter-based conflict detection, which often falsely report conflicts between transactions. Second, we propose a best-effort HTM that utilizes the new scalable conflict detection protocol, termed EazyHTM. EazyHTM allows parallel commits for all non-conflicting transactions, and generally simplifies transaction commits. Finally, we propose an unbounded HTM that extends and improves the initial protocol for conflict management, and we name it EcoTM. EcoTM features precise conflict detection, and it efficiently supports large as well as small and short transactions. The key idea of EcoTM is to leverage an observation that very few locations are actually conflicting, even if applications have high contention. In EcoTM, each core locally detects if a cache line is non-conflicting, and conflict detection mechanism is invoked only for the few potentially conflicting cache lines.La Sincronización tradicional basada en los cerrojos de exclusión mutua (locks) serializa los accesos a las secciones críticas protegidas este cerrojo. La utilización de varios cerrojos en forma concurrente y/o paralela aumenta la posibilidad de entrar en abrazo mortal (deadlock) o en un bloqueo activo (livelock) en el programa, está es una de las razones por lo cual programar en forma paralela resulta ser mucho mas dificultoso que programar en forma secuencial. La memoria transaccional (TM) es un paradigma prometedor para la programación paralela, que ofrece una alternativa a los cerrojos. La memoria transaccional tiene muchas ventajas desde el punto de vista tanto práctico como teórico. TM elimina el riesgo de bloqueo mutuo y de bloqueo activo, mientras que proporciona una semántica de atomicidad, coherencia, aislamiento con características similares a las secciones críticas. TM ejecuta especulativamente una serie de accesos a la memoria como una transacción atómica. Los cambios especulativos de la transacción se mantienen privados hasta que se confirma la transacción. Si una transacción entra en conflicto con otra transacción o sea que alguna de ellas escribe en una dirección que la otra leyó o escribió, o se entra en un abrazo mortal o en un bloqueo activo, el sistema de TM aborta la transacción y revierte los cambios especulativos. Para ser eficaz, una implementación de TM debe proporcionar un alto rendimiento y escalabilidad. Las implementaciones de TM en el software (STM) no proporcionan este desempeño deseable, en cambio, las mplementaciones de TM en hardware (HTM) tienen mejor desempeño y una escalabilidad relativamente buena, debido a su mejor control de los recursos de hardware y que la resolución de los conflictos así el mantenimiento y gestión de los datos se hace en hardware. Sin embargo, muchos de los sistemas de HTM están limitados a los recursos de hardware disponibles, por ejemplo el tamaño de las caches privadas, y dependen de mecanismos de software para cuando esos límites son sobrepasados. Estos sistemas HTM, llamados best-effort HTM no son deseables, ya que obligan al programador a pensar en términos de los límites existentes en el hardware que se esta utilizando, así como en el sistema de STM que se llama cuando los recursos son sobrepasados. Además, tiene que resolver que transacciones hardware y software se ejecuten concurrentemente. En cambio, los sistemas de HTM ilimitados soportan un numero de operaciones ilimitadas o sea no están restringidos a límites impuestos artificialmente por el hardware, como ser el tamaño de las caches o buffers internos. Los sistemas HTM ilimitados por lo general requieren protocolos complejos o mecanismos muy costosos para la detección de conflictos y el mantenimiento de versiones de los datos entre las transacciones. Por otra parte, la ejecución de transacciones es a menudo mucho más lenta que en una ejecución sobre un sistema de HTM que este limitado. Esto es debido al que los mecanismos utilizados en el HTM limitado trabaja con conjuntos de datos relativamente pequeños que caben o están muy cerca del núcleo del procesador. En esta tesis estudiamos implementaciones de TM en hardware. Presentaremos tres contribuciones principales: Primero, mejoramos el rendimiento general de los sistemas, al proponer un protocolo escalable para la gestión de conflictos. El protocolo detecta los conflictos de forma precisa, en contraste con otras técnicas basadas en filtros Bloom, que pueden reportar conflictos falsos entre las transacciones. Segundo, proponemos un best-effort HTM que utiliza el nuevo protocolo escalable detección de conflictos, denominado EazyHTM. EazyHTM permite la ejecución completamente paralela de todas las transacciones sin conflictos, y por lo general simplifica la ejecución. Por último, proponemos una extensión y mejora del protocolo inicial para la gestión de conflictos, que llamaremos EcoTM. EcoTM cuenta con detección de conflictos precisa, eficiente y es compatible tanto con transacciones grandes como con pequeñas. La idea clave de EcoTM es aprovechar la observación que en muy pocas ubicaciones de memoria aparecen los conflictos entre las transacciones, incluso en aplicaciones tienen muchos conflictos. En EcoTM, cada núcleo detecta localmente si la línea es conflictiva, además existe un mecanismo de detección de conflictos detallado que solo se activa para las pocas líneas de memoria que son potencialmente conflictivas

Stretching the capacity of Hardware Transactional Memory in IBM POWER architectures

The hardware transactional memory (HTM) implementations in commercially available processors are significantly hindered by their tight capacity constraints. In practice, this renders current HTMs unsuitable to many real-world workloads of in-memory databases. This paper proposes SI-HTM, which stretches the capacity bounds of the underlying HTM, thus opening HTM to a much broader class of applications. SI-HTM leverages the HTM implementation of the IBM POWER architecture with a software layer to offer a single-version implementation of Snapshot Isolation. When compared to HTM- and software-based concurrency control alternatives, SI-HTM exhibits improved scalability, achieving speedups of up to 300% relatively to HTM on in-memory database benchmarks

A new approach to reversible computing with applications to speculative parallel simulation

In this thesis, we propose an innovative approach to reversible computing that shifts the focus from the operations to the memory outcome of a generic program. This choice allows us to overcome some typical challenges of "plain" reversible computing. Our methodology is to instrument a generic application with the help of an instrumentation tool, namely Hijacker, which we have redesigned and developed for the purpose. Through compile-time instrumentation, we enhance the program's code to keep track of the memory trace it produces until the end. Regardless of the complexity behind the generation of each computational step of the program, we can build inverse machine instructions just by inspecting the instruction that is attempting to write some value to memory. Therefore from this information, we craft an ad-hoc instruction that conveys this old value and the knowledge of where to replace it. This instruction will become part of a more comprehensive structure, namely the reverse window. Through this structure, we have sufficient information to cancel all the updates done by the generic program during its execution. In this writing, we will discuss the structure of the reverse window, as the building block for the whole reversing framework we designed and finally realized. Albeit we settle our solution in the specific context of the parallel discrete event simulation (PDES) adopting the Time Warp synchronization protocol, this framework paves the way for further general-purpose development and employment. We also present two additional innovative contributions coming from our innovative reversibility approach, both of them still embrace traditional state saving-based rollback strategy. The first contribution aims to harness the advantages of both the possible approaches. We implement the rollback operation combining state saving together with our reversible support through a mathematical model. This model enables the system to choose in autonomicity the best rollback strategy, by the mutable runtime dynamics of programs. The second contribution explores an orthogonal direction, still related to reversible computing aspects. In particular, we will address the problem of reversing shared libraries. Indeed, leading from their nature, shared objects are visible to the whole system and so does every possible external modification of their code. As a consequence, it is not possible to instrument them without affecting other unaware applications. We propose a different method to deal with the instrumentation of shared objects. All our innovative proposals have been assessed using the last generation of the open source ROOT-Sim PDES platform, where we integrated our solutions. ROOT-Sim is a C-based package implementing a general purpose simulation environment based on the Time Warp synchronization protocol

Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis

Reactive molecular dynamics (MD) simulation is a powerful research tool for describing chemical reactions. We eliminate the speed-limiting charge iteration in MD with a novel extended-Lagrangian scheme. The extended-Lagrangian reactive MD (XRMD) code drastically improves energy conservation while substantially reducing time-to-solution. Furthermore, we introduce a new polarizable charge equilibration (PQEq) model to accurately predict atomic charges and polarization. The XRMD code based on hybrid message passing+multithreading achieves a weak-scaling parallel efficiency of 0.977 on 786 432 IBM Blue Gene/Q cores for a 67.6 billion-atom system. The performance is portable to the second-generation Intel Xeon Phi, Knights Landing. Blue Gene/Q simulations for the computational synthesis of materials via novel exfoliation mechanisms for synthesizing atomically thin transition metal dichalcogenide layers will dominate nanomaterials science in this century

Techniques to improve concurrency in hardware transactional memory

Transactional Memory (TM) aims to make shared memory parallel programming easier by abstracting away the complexity of managing shared data. The programmer defines sections of code, called transactions, which the TM system guarantees that will execute atomically and in isolation from the rest of the system. The programmer is not required to implement such behaviour, as happens in traditional mutual exclusion techniques like locks - that responsibility is delegated to the underlying TM system. In addition, transactions can exploit parallelism that would not be available in mutual exclusion techniques; this is achieved by allowing optimistic execution assuming no other transaction operates concurrently on the same data. If that assumption is true the transaction commits its updates to shared memory by the end of its execution, otherwise, a conflict occurs and the TM system may abort one of the conflicting transactions to guarantee correctness; the aborted transaction would roll-back its local updates and be re-executed. Hardware and software implementations of TM have been studied in detail. However, large-scale adoption of software-only approaches have been hindered for long due to severe performance limitations. In this thesis, we focus on identifying and solving hardware transactional memory (HTM) issues in order to improve concurrency and scalability. Two key dimensions determine the HTM design space: conflict detection and speculative version management. The first determines how conflicts are detected between concurrent transactions and how to resolve them. The latter defines where transactional updates are stored and how the system deals with two versions of the same logical data. This thesis proposes a flexible mechanism that allows efficient storage and access to two versions of the same logical data, improving overall system performance and energy efficiency. Additionally, in this thesis we explore two solutions to reduce system contention - circumstances where transactions abort due to data dependencies - in order to improve concurrency of HTM systems. The first mechanism provides a suitable design to apply prefetching to speed-up transaction executions, lowering the window of time in which such transactions can experience contention. The second is an accurate abort prediction mechanism able to identify, before a transaction's execution, potential conflicts with running transactions. This mechanism uses past behaviour of transactions and locality in memory references to infer predictions, adapting to variations in workload characteristics. We demonstrate that this mechanism is able to manage contention efficiently in single-application and multi-application scenarios. Finally, this thesis also analyses initial real-world HTM protocols that recently appeared in market products. These protocols have been designed to be simple and easy to incorporate in existing chip-multiprocessors. However, this simplicity comes at the cost of severe performance degradation due to transient and persistent livelock conditions, potentially preventing forward progress. We show that existing techniques are unable to mitigate this degradation effectively. To deal with this issue we propose a set of techniques that retain the simplicity of the protocol while providing improved performance and forward progress guarantees in a wide variety of transactional workloads

Measurement, Modeling, and Characterization for Energy-Efficient Computing

The ever-increasing ecological footprint of Information Technology (IT) sector coupled with adverse effects of high power consumption on electronic circuits has increased the significance of energy-efficient computing in the last decade. Making energy-efficient computing a norm rather than an exception requires that system designers and programmers understand the energy implications of their design and implementation choices. This necessitates a detailed view of system’s energy expenditure and/or power consumption. We explore this aspect of energy-efficient computing in this thesis through power measurement, power modeling, and energy characterization.First, we present a quantitative comparison between power measurement data collected for computer systems using four techniques: a power meter at wall outlet, currenttransducers at ATX power rails, CPU voltage regulator’s current monitor, and Intel’s proprietary RAPL (Running Average Power Limit) interface. We compare them for accuracy, sensitivity and accessibility.Second, we present two different methodologies to model processor power consumption. The first model estimates power consumption at the granularity of individualcores using per-core performance events and temperature sensors. We validate the methodology on six different platforms and show that our model estimates power consumption with high accuracy across all platforms consistently. To understand the energy expenditure trends across different frequencies and different degrees of parallelism, we need to model power at a much finer granularity. The second power model addresses this issue by estimating static and dynamic power consumption for individual cores and the uncore. We validate this model on Intel’s Haswell platform for single-threaded and multi-threaded benchmarks. We use this power model to characterize energy efficiency of frequency scaling on Haswell microarchitecture and use the insights to implementa low overhead DVFS scheduler. We also characterize the energy efficiency of thread scaling using the power model and demonstrate how different communication parametersand microarchitectural traits affect application’s energy when it scales.Finally, we perform detailed performance and energy characterization of Intel’s RestrictedTransactional Memory (RTM).We use TinySTM software transactional memory(STM) system to benchmark RTM’s performance against competing STM alternatives.We use microbenchmarks and STAMP benchmark suite to compare RTM an STM performanceand energy behavior. We quantify the RTM hardware limitations and identifyconditions required for RTM to outperform STM